Data standardization by the HUPO-PSI: how has the community benefitted?

The groundwork allowing the systematic capture of proteomics data has now largely been completed, with the design and publication of exchange formats and interchange standards by the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI). Our focus can now shift to gathering the ever-increasing amounts of generated data, and finding novel ways to catalog and present it so that a deeper understanding of basic science, health, and disease can be gained by scientists mining these increasingly rich resources.

[1]  Sylvie Ricard-Blum,et al.  MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions , 2009, Bioinform..

[2]  Lennart Martens,et al.  The PSI formal document process and its implementation on the PSI website , 2007, Proteomics.

[3]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[4]  Allan Kuchinsky,et al.  Exploring Biological Networks with Cytoscape Software , 2008, Current protocols in bioinformatics.

[5]  Gary D Bader,et al.  BMC Biology BioMed Central , 2007 .

[6]  D. Scholtens,et al.  A general pipeline for quality and statistical assessment of protein interaction data using R and Bioconductor , 2009, Nature Protocols.

[7]  Ioannis Xenarios,et al.  DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions , 2002, Nucleic Acids Res..

[8]  Chris F. Taylor,et al.  A common open representation of mass spectrometry data and its application to proteomics research , 2004, Nature Biotechnology.

[9]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[10]  Henning Hermjakob,et al.  Submit Your Interaction Data the IMEx Way , 2007, Proteomics.

[11]  Lennart Martens,et al.  HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy , 2006, Proteomics.

[12]  Henning Hermjakob,et al.  Annual Spring Meeting of the Proteomics Standards Initiative , 2009, Proteomics.

[13]  Lennart Martens,et al.  A guide to the Proteomics Identifications Database proteomics data repository , 2009, Proteomics.

[14]  Olga V. Matveeva,et al.  Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome , 2004, BMC Bioinformatics.

[15]  Chris F. Taylor,et al.  Guidelines for reporting the use of mass spectrometry informatics in proteomics , 2008, Nature Biotechnology.

[16]  C. Sander,et al.  The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data , 2004, Nature Biotechnology.

[17]  Peter Uetz,et al.  MPIDB: the microbial protein interaction database , 2008, Bioinform..

[18]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[19]  Chris F. Taylor,et al.  Guidelines for reporting the use of gel electrophoresis in proteomics , 2008, Nature Biotechnology.

[20]  Nigel W. Hardy,et al.  Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project , 2008, Nature Biotechnology.

[21]  Lennart Martens,et al.  The PSI semantic validator: A framework to check MIAPE compliance of proteomics data , 2009, Proteomics.

[22]  Maria Victoria Schneider,et al.  MINT: a Molecular INTeraction database. , 2002, FEBS letters.

[23]  Lennart Martens,et al.  PRIDE Converter: making proteomics data-sharing easy , 2009, Nature Biotechnology.

[24]  E. Birney,et al.  The International Protein Index: An integrated database for proteomics experiments , 2004, Proteomics.

[25]  Eugene A. Kapp,et al.  Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly‐available database , 2005, Proteomics.

[26]  Hans-Werner Mewes,et al.  MPact: the MIPS protein interaction resource on yeast , 2005, Nucleic Acids Res..

[27]  Christine Hoogland,et al.  MIAPEGelDB, a web-based submission tool and public repository for MIAPE gel electrophoresis documents. , 2008, Journal of proteomics.

[28]  Sandra Orchard Ending the "publish and vanish" culture: how the data standardization process will assist in data harvesting. , 2009, Journal of proteome research.